MolNFT v1 · #41126 · protein
Structure of a 9-subunit archaeal exosome
2JE6 · Exosome complex exonuclease 2: “Structure of a 9-subunit archaeal exosome”. X-ray diffraction, 1 ligand (CL), 6 pockets (best druggability 0.76). MolNFT v1 #41126 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2JE6
- Type
- protein
- Length
- 715 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exosome complex exonuclease 2; Exosome complex exonuclease 1; Exosome complex RNA-binding…
- EC
- 3.1.13.-
- UniProt
- Q9UXC0, Q9UXC2, Q9UXC4
- Ligands
- CL
- Pockets
- 6 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 25% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exosome complex exonuclease 2 (EC 3.1.13.-) | protein | 274 | 28% helix, 35% strand | Q9UXC0 |
| B | Exosome complex exonuclease 1 (EC 3.1.13.-) | protein | 234 | 32% helix, 33% strand | Q9UXC2 |
| I | Exosome complex RNA-binding protein 1 (EC 3.1.13.-) | protein | 207 | 13% helix, 36% strand | Q9UXC4 |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
- 1PE · Pentaethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 934 | 0.76 | 0.79 | 74 | empty |
| 2 | 395 | 0.58 | 0.75 | 55 | CL |
| 3 | 118 | 0.57 | 0.84 | 19 | empty |
| 4 | 170 | 0.46 | 0.75 | 26 | empty |
| 5 | 195 | 0.44 | 0.73 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1889 Ų buried · 42 hydrogen bonds · protein-protein
- A–I · 285 Ų buried · 0 hydrogen bonds · protein-protein
- B–I · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2JE6 · Structure of a 9-subunit archaeal exosome · the same entry in another collection · chain A against A, TM-score 1.00
- Q9UXC2 · AlphaFold monomer V2.0 prediction for exosome complex component RRP41 (Q9UXC2) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9UXC0 · AlphaFold monomer V2.0 prediction for exosome complex component RRP42 (Q9UXC0) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9UXC4 · AlphaFold monomer V2.0 prediction for exosome complex component RRP4 (Q9UXC4) · a predicted model of the same protein · chain I against A, TM-score 0.85
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9UXC0
- Every structure of UniProt Q9UXC2
- Every structure of UniProt Q9UXC4
- Elsewhere: RCSB PDB 2JE6 · PDBe 2JE6 · UniProt Q9UXC0 · UniProt Q9UXC2 · UniProt Q9UXC4
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